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Started by upstream project "BIOFORMATS-test-repo" build number 276 originally caused by: Started by upstream project "Trigger" build number 297 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins10154213166809965488.sh + '[' samples = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_43481_merge_ci -v /uod/idr/repos/curated/samples:/data -v /uod/idr-scratch/merge-ci/curated/samples:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test test-automated: [testng] File leak detector installed [testng] 00:35:17,243 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:35:17,245 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:35:17,245 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:35:17,247 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:35:17,247 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:35:17,247 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:35:17,248 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:35:17,248 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:35:17,248 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:35:17,249 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:35:17,249 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:35:17,249 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:35:17,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:35:17,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:35:17,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:35:17,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:35:17,552 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:35:17,552 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:35:17,552 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:35:17,552 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:35:17,553 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:35:17,553 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:35:17,554 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 306 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-02 00:35:17,569] [main] java.version = 1.8.0_342 [testng] 00:35:17,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:35:17,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:17,628 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-02_00-35-17.log] [testng] 00:35:17,630 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-02 00:35:17,632] [main] testng.directory = /data [testng] [2024-12-02 00:35:17,632] [main] testng.configDirectory = /config [testng] [2024-12-02 00:35:17,645] [main] testng.multiplier = 1.0 [testng] [2024-12-02 00:35:17,645] [main] testng.in-memory = false [testng] [2024-12-02 00:35:17,645] [main] testng.allow-missing = false [testng] [2024-12-02 00:35:17,645] [main] user.language = fr [testng] [2024-12-02 00:35:17,645] [main] user.country = FR [testng] [2024-12-02 00:35:17,646] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-02 00:36:04,914] [main] ---------------------------------------- [testng] [2024-12-02 00:36:04,914] [main] Total files: 164 [testng] [2024-12-02 00:36:04,915] [main] Scan time: 47.268 s (288 ms/file) [testng] [2024-12-02 00:36:04,915] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-02 00:37:30,562] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 00:37:30,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:37:30,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:30,563 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-02_00-37-30.log] [testng] 00:37:30,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b6d144e - End of configuration. [testng] [2024-12-02 00:37:30,938] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:37:30,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:37:30,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:30,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-02_00-37-30.log] [testng] 00:37:30,939 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a0d8a2a - End of configuration. [testng] [2024-12-02 00:37:31,390] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 00:37:31,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:37:31,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:31,391 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-02_00-37-31.log] [testng] 00:37:31,391 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70dfa199 - End of configuration. [testng] [2024-12-02 00:37:31,772] [pool-1-thread-10] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] 00:37:31,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:37:31,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:31,773 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-02_00-37-31.log] [testng] 00:37:31,773 |-INFO in ch.qos.logback.core.sift.SiftProcessor@470b5da5 - End of configuration. [testng] [2024-12-02 00:37:32,486] [pool-1-thread-9] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 00:37:32,487 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:37:32,487 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:32,487 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-02_00-37-32.log] [testng] 00:37:32,488 |-INFO in ch.qos.logback.core.sift.SiftProcessor@554e131 - End of configuration. [testng] [2024-12-02 00:37:32,907] [pool-1-thread-8] Initializing /data/ome/C1midmusnorm.lsm: [testng] 00:37:32,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:37:32,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:32,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-02_00-37-32.log] [testng] 00:37:32,909 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65457f80 - End of configuration. [testng] [2024-12-02 00:37:33,320] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp: [testng] 00:37:33,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:37:33,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:33,321 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-02_00-37-33.log] [testng] 00:37:33,321 |-INFO in ch.qos.logback.core.sift.SiftProcessor@265e8ef7 - End of configuration. [testng] [2024-12-02 00:37:33,383] [pool-1-thread-6] Initializing /data/TAABA/TAABA.pattern: [testng] 00:37:33,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:37:33,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:33,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-02_00-37-33.log] [testng] 00:37:33,386 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c2c77aa - End of configuration. [testng] [2024-12-02 00:37:55,117] [pool-1-thread-5] Initializing /data/ome/tiffany.color.tiff: [testng] 00:37:55,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:37:55,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:55,118 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-02_00-37-55.log] [testng] 00:37:55,119 |-INFO in ch.qos.logback.core.sift.SiftProcessor@462c436b - End of configuration. [testng] [2024-12-02 00:37:56,640] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] 00:37:56,640 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:37:56,640 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:56,641 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-02_00-37-56.log] [testng] 00:37:56,641 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66b12d5a - End of configuration. [testng] [2024-12-02 00:37:56,929] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 00:37:56,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:37:56,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:56,930 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-02_00-37-56.log] [testng] 00:37:56,931 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e03210d - End of configuration. [testng] [2024-12-02 00:37:57,104] [pool-1-thread-2] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:37:57,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:37:57,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:57,104 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-02_00-37-57.log] [testng] 00:37:57,105 |-INFO in ch.qos.logback.core.sift.SiftProcessor@700c1a6e - End of configuration. [testng] [2024-12-02 00:38:01,898] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-12-02 00:38:02,457] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-12-02 00:38:02,602] [pool-1-thread-3] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-12-02 00:38:03,310] [pool-1-thread-7] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-12-02 00:38:03,568] [pool-1-thread-8] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-12-02 00:38:03,898] [pool-1-thread-12] Initializing /data/ome/654Atemp.stk: [testng] [2024-12-02 00:38:05,376] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-12-02 00:38:06,253] [pool-1-thread-7] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-12-02 00:38:07,486] [pool-1-thread-1] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-12-02 00:38:08,108] [pool-1-thread-10] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-12-02 00:38:08,614] [pool-1-thread-2] Initializing /data/ome/worm.tiff: [testng] [2024-12-02 00:38:09,714] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-12-02 00:38:10,643] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-12-02 00:38:11,021] [pool-1-thread-5] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-12-02 00:38:11,420] [pool-1-thread-8] Initializing /data/ome/embryo.lsm: [testng] [2024-12-02 00:38:11,742] [pool-1-thread-3] Initializing /data/ome/C1.lsm: [testng] [2024-12-02 00:38:13,578] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-12-02 00:38:15,515] [pool-1-thread-1] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-12-02 00:38:16,691] [pool-1-thread-10] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-12-02 00:38:17,549] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-12-02 00:38:17,784] [pool-1-thread-8] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-12-02 00:38:18,357] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-12-02 00:38:18,487] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-12-02 00:38:19,751] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-12-02 00:38:20,153] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-12-02 00:38:21,103] [pool-1-thread-12] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-12-02 00:38:21,959] [pool-1-thread-9] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-12-02 00:38:22,544] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-12-02 00:38:22,619] [pool-1-thread-10] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-12-02 00:38:23,300] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-12-02 00:38:24,075] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-12-02 00:38:25,403] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-12-02 00:38:25,633] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-12-02 00:38:26,304] [pool-1-thread-10] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-12-02 00:38:27,085] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-12-02 00:38:27,555] [pool-1-thread-9] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-12-02 00:38:28,415] [pool-1-thread-4] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-12-02 00:38:28,676] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-12-02 00:38:28,850] [pool-1-thread-3] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-12-02 00:38:30,157] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern: [testng] [2024-12-02 00:38:36,083] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-12-02 00:38:37,068] [pool-1-thread-4] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-12-02 00:38:37,182] [pool-1-thread-5] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-12-02 00:38:38,315] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-12-02 00:38:39,432] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-12-02 00:38:39,656] [pool-1-thread-10] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-12-02 00:38:40,786] [pool-1-thread-4] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 4 minutes 38 seconds Finished: SUCCESS